| | --- |
| | license: mit |
| | task_categories: |
| | - other |
| | tags: |
| | - biology |
| | - genomics |
| | - synteny |
| | - plants |
| | pretty_name: Plant Microsynteny Data |
| | size_categories: |
| | - 1B<n<10B |
| | --- |
| | |
| | # Plant Microsynteny Dataset (plant-msyn-data) |
| |
|
| | Pre-computed MCscan protein-based synteny analysis results for 30+ plant genomes. |
| |
|
| | ## Dataset Structure |
| |
|
| | ``` |
| | plant-msyn-data/ |
| | ├── mcscan_results/ |
| | │ ├── bed_files/ # Gene position files (*.bed) + database_genomes.txt whitelist |
| | │ ├── i1_blocks/ # Synteny block files (*.i1.blocks) |
| | │ ├── lifted_anchors/ # Syntenic anchor pair files (*.lifted.anchors) |
| | │ ├── last_filtered_by_i1/ # I1-filtered LAST alignments |
| | │ ├── pep_files/ # Protein FASTA files (*.pep) |
| | │ ├── custom_meta/ # Custom genome metadata (user uploads) |
| | │ └── custom_synteny_meta/ # Custom synteny project metadata |
| | ├── sql/ |
| | │ ├── search_catalogs/ # Per-genome SQLite catalogs for fast gene lookups |
| | │ └── plantmsyn_metadata.db # Central metadata database |
| | └── annotations/ |
| | └── [species_name]/ |
| | └── gene_annotation.tsv # Gene functional descriptions |
| | ``` |
| |
|
| | ## Supported Genomes |
| |
|
| | The dataset includes synteny data for 30+ plant genomes including: |
| | - Barley (*Hordeum vulgare*) |
| | - Wheat (*Triticum aestivum*) |
| | - Rice (*Oryza sativa*) |
| | - Maize (*Zea mays*) |
| | - Arabidopsis (*Arabidopsis thaliana*) |
| | - And 25+ more species |
| |
|
| | ## Usage |
| |
|
| | This dataset is designed to be used with the [Plant-mSyn web application](https://huggingface.co/spaces/yoshigold/plant-msyn). |
| |
|
| | To use programmatically: |
| |
|
| | ```python |
| | from huggingface_hub import snapshot_download |
| | |
| | # Download the full dataset |
| | local_path = snapshot_download( |
| | repo_id="yoshigold/plant-msyn-data", |
| | repo_type="dataset" |
| | ) |
| | ``` |
| |
|
| | ## File Formats |
| |
|
| | ### BED Files (`*.bed`) |
| | Tab-separated files with gene positions: |
| | - Column 1: Chromosome |
| | - Column 2: Start position |
| | - Column 3: End position |
| | - Column 4: Gene ID |
| | - Column 5: Score |
| | - Column 6: Strand |
| | |
| | ### Blocks Files (`*.i1.blocks`) |
| | Tab-separated synteny block definitions linking genes between species. |
| |
|
| | ### Annotation Files (`gene_annotation.tsv`) |
| | Tab-separated files with: |
| | - Column 1: gene (Gene ID) |
| | - Column 2: description (Functional annotation) |
| | |
| | ## Citation |
| | |
| | If you use this dataset, please cite: |
| | - MCscan/JCVI: Tang et al. (2008) Synteny and Collinearity in Plant Genomes |
| | |
